At broad spatial scales, primary productivity in lakes is known to increase in concert with nutrients, and variables that may disrupt or modify the tight coupling of nutrients and algae are of increasing interest, particularly for those shifting with climate change. Storms may disrupt algae–nutrient relationships, but the expected effects differ between winter and summer seasons, particularly for seasonally ice-covered lakes. In winter, storms can dramatically change the under-ice light environment, creating light limitation that disrupts algae–nutrient relationships. Further, storms can bring both snow that blocks light and also wind that blows snow off of ice. In open water conditions, storms may promote turbulence and external nutrient loading. Here, we test the hypotheses that winter and summer storms differentially affect algae–nutrient relationships across 84 seasonally ice-covered lakes included in the Ecology Under Lake Ice dataset. While nutrients explained most of the variation in chlorophyll across these lakes, we found that secondary drivers differed between seasons. Under-ice chlorophyll was higher under a variety of precipitation and wind conditions that tend to promote snow-free clear ice, highlighting the importance of light as a limiting factor for algal growth during winter. In summer, higher water temperatures and storms corresponded with higher chlorophyll. Our study suggests that examining ice-covered lakes in a gradient from the perennial ice cover of the poles to the intermittent ice cover of lower latitudes would yield key information on the shifts in light and nutrient limitation that control algal biomass.